Study on the active ingredients of Shenghui decoction inhibiting acetylcholinesterase based on molecular docking and molecular dynamics simulation

Abstract

We aim to investigate the mechanism and effective components of Shenghui decoction (SHD), which has been shown to inhibit acetylcholinesterase (AChE) through molecular docking (MD) and molecular dynamics simulation (MDS). The effective ingredients in SHD were collected through the TCMSP database and literature review. All components were docked with AChE using CDOCKER. Receptor ligand interaction analysis was performed for the optimal ligand. Two simulation models (model I and II) containing AChE and acetylcholine (ACh) were constructed, in which model II contained the best-docked ligand. Perform 90ns MDS on 2 models. After the simulation, the distance between ACh and AChE peripheral active sites were calculated in both models. The root mean square deviation (RMSD) curve of ligand and receptor, the radius of gyration (Rog) of the receptor, the distance between ligand center and binding site center, and the binding energy of ligand and receptor were calculated in model II. 98 ingredients of SHD were collected, and the best ligand was Tumulosic acid. The residues that form conventional hydrogen bonds between AChE and Tumulosic acid include Tyr132 and Glu201. MDS revealed that ACh could bind to AChE active site in model I. In model II, ACh cannot bind to the binding cavity because the ligand occupies the active site. The RMSD of AChE and Tumulosic acid tends to be stable, the Rog curve of AChE is relatively stable, and the distance between ligand and binding cavity does not fluctuate greatly, indicating that the structure of receptor and ligand is relatively stable. The binding energy of AChE and Tumulosic acid was −24.14 ± 2.46 kcal/mol. SHD contains many effective ingredients that may inhibit AChE activity. Tumulosic acid can occupy the binding site to prevent ACh from entering the chemical domain, thus exerting AChE inhibitory effect.